Hox cluster disintegration

Posted 2 September 2004 by PZ Myers

↗ The current version of this post is on the live site: https://pandasthumb.org/archives/2004/09/hox-cluster-dis.html

Hox genes are metazoan pattern forming genes—genes that are universally associated with defining the identities of regions of the body. There are multiple Hox genes present, and one of their unusual properties is that they are clustered and expressed colinearly. That is, they are found in ordered groups on the chromosome, and that the gene on one end is typically turned on first and expressed at the head end of the embryo, the next gene in order is turned on slightly later and expressed further back, and so on in sequence. That the tidy sequential order on the chromosome is associated with an equally tidy spatial and temporal pattern of expression in the body has always been one of the more fascinating aspects of these genes, and they are one of the few cases where we see an echo of phenotypic form comprehensibly laid out in the DNA.

However, there are some exceptions to the tidy clustering, and they occur right in two animals that have been central to developmental/genetic research, Caenorhabditis elegans and Drosophila melanogaster. These animals have broken clusters. Almost everywhere else, the Hox genes are ordered in one place, but in two of the most common research organisms, they've been split apart into two groups…so what's going on? We have what looks a little bit like a universal rule in genetic organization, and then it gets violated with seemingly little consequence. How do worms and flies get away with it?

One way to find out is to look for more exceptions to Hox ordering, and here's a doozy: an animal, the tunicate Oikopleura dioica, has blown its Hox gene clusters to flinders and scattered the individual Hox genes all over its genome, with no detectable linkage between them.

Continue reading "Hox cluster disintegration" (on Pharyngula)

4 Comments

Steve · 2 September 2004

As a physics student who learns bio in bits an pieces as he needs to do biophys research, I haven't come across anything about how the physical layout of genes relates to their expression. Except one tangential thing--Is it true that mitochondrial genes have gradually shifted to the cell genomes? Why would this happen?

Reed A. Cartwright · 2 September 2004

As a physics student who learns bio in bits an pieces as he needs to do biophys research, I haven't come across anything about how the physical layout of genes relates to their expression. Except one tangential thing---Is it true that mitochondrial genes have gradually shifted to the cell genomes? Why would this happen?
— Steve

There are a few hypotheses. Intracellular Competition Mitochondria that shed genes have less DNA and can replicate faster than other mitochondria. Eventually these faster replicating mitochondria outbread their competition, producing a cell with smaller mitochondria. Avoidance of Mutation Nuclear genes have lower mutation rates and are more faithful than mitochondrial genes. Selection against deliterious mutations thus favors cells with nuclear copies. Efficient Factories Mitochondria use part of the energy they produce to replicate, etc. The more efficient, i.e. smaller, mitochondria are the more energy there is for the cell. Therefore, the smaller the mitochondria the faster the cell can divide and thus out compete other cells without efficient mitochondria. (This is one I came up with two years ago. I'm not sure whereelse biologists have proposed it.) I'm pretty sure there is another one about intercellular competition that I'm forgetting.

Wesley R. Elsberry · 2 September 2004

Larvaceans are cool. One of my fellow students way back when did a class project on them and had to jury-rig a tank that would keep them alive for at least a few weeks. She ended up with a cylindrical tank that had a continuous counter-clockwise current going.

Steve · 2 September 2004

Thanks, Reed, those are interesting ideas. I think it's kind of mind blowing that mitochondria (and hydrogenosomes too I think) are evolving within the environment of the cell. And with all that oxidative craziness going on in them, it's really cool that they are getting some of their sensitive manufacturing done off-site.